Abstract 1506: Decoding multi-omics genetic profiling reveals heterogeneity in adult pan-gliomas
Authors: Takuma Nakashima, Yusuke Funakoshi, Atsuhito Uneda, Yuriko Sugihara, Shohei Nambu, Manabu Kinoshita, Yoshiki Arakawa, Shota Tanaka, Joji Ishida, Ryuta Saito, Ryosuke Hanaya, Koji Yoshimoto, Yoshitaka Narita, Hiromichi Suzuki
Journal: Cancer Research (2023)

Abstract Adult-type diffuse gliomas (Glioblastoma (GBM), Astrocytoma, Oligodendroglioma) are the most common malignant brain tumor in adults with dismal prognoses. Recent large-scale genomic studies have established molecular classification of glioma based on coding mutations and copy number variations. However, whole-genome landscape and multi-omics profiles of gliomas are not well analyzed. To understand the multi-omics genetic landscape of gliomas, we performed deep whole-genome sequencing (≥ ×120 coverage) of 357 cases with adult-type diffuse gliomas (162 GBMs, 96 astrocytomas, 99 oligodendrogliomas) along with EPIC DNA methylation profiling. RNA-seq, whole-genome bisulfate sequencing, and assay for transposase-accessible chromatin with sequencing (ATAC-seq) were performed on 349, 40, and 40 of these tumors, respectively. Deep WGS delineated a fine view of clonal architecture demonstrating mutational order during tumor initiation of each glioma. Mutational signature varies between clonal and subclonal mutations, supporting a model that tumors acquire genetic alterations by distinct mechanisms based on their developmental stage. Structural variants (SVs) are more frequently detected in higher malignant gliomas. While a complex SV is rare in Astrocytoma and Oligodendroglioma (35% of samples), a large proportion of GBM cases (85%) have complex SV with ≥ 10 breakpoints, which involves multiple different chromosomes including driver genes. CDKN2A homozygous deletions and focal CDK4 amplifications are often induced by complex SVs in GBM. These results suggest that complex SVs could play a pivotal role in the initiation and progression of GBM. Integrative analysis of transcriptomic and epigenomic profiles by similarity network fusion (SNF) identifies homogenous clusters in each glioma where those clusters are associated with mutational and SV signatures, suggesting that specific cell states may have distinct sensitivities to mutational processes. In oligodendrogliomas, the SNF classification detected a cluster with poor prognosis which has an enrichment of stem cell-like signature by CIBERSORTx deconvolution analysis. ATAC-seq demonstrated distinct features of genome-wide chromatin accessibility in each glioma which may reflect the difference of cell of the origin. Most of the focally amplified genes have open chromatin status suggesting that tumors take advantage of not only gene duplication but also a transcriptional activity to activate driver genes. Our integrated analysis uncovers molecular mechanisms of gliomas which will help to understand glioma-genesis. Citation Format: Takuma Nakashima, Yusuke Funakoshi, Atsuhito Uneda, Yuriko Sugihara, Shohei Nambu, Manabu Kinoshita, Yoshiki Arakawa, Shota Tanaka, Joji Ishida, Ryuta Saito, Ryosuke Hanaya, Koji Yoshimoto, Yoshitaka Narita, Hiromichi Suzuki. Decoding multi-omics genetic profiling reveals heterogeneity in adult pan-gliomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1506.